Interpreting the SNP Data in MGI
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This Help document answers the following questions about the SNP Data in MGI report:

See also:

What SNP data does the MGI database contain?

What SNP data does the MGI database NOT contain?

MGI does not load the following data:


Where does MGI get mouse SNP data and when does it load this data?

MGI loads mouse SNP data from dbSNP at NCBI in conjunction with new dbSNP build releases.

How can I tell which dbSNP build the data comes from?

The dbSNP build number appears at the top of the SNP Data in MGI Report in the Provider/Version column.

What's in the SNP Data in MGI report?

The report is a summary of the dbSNP data in the MGI database and contains information about the:

The report contains links to:


How do I interpret the data in this report?

Provider/Version | Description | Statistics | Assays (ss) per submitter | RefSNPs (rs) per strain by chromosome
The name of the provider (dbSNP at NCBI) and beside it, a link to the provider's web site. Beneath this is the dbSNP build number that comprises the SNP data in MGI.
Description Details about MGI SNP data, Reference SNPs (rs), submitted SNP assays (ss), and what SNP data the MGI database does and does not contain. Beneath these details are links to statistics for this build at NCBI dbSNP and to a list of all mouse Reference SNPs from dbSNP not loaded (at MGI) plus the reason for the omission.
Statistics All data values are from the most current dbSNP build loaded into the MGI database. Note: Some values for number of SNPs in MGI may differ from Provider values. See Description for details. For more information, see dbSNP Data Statistics.
Total Assays (ss): Number of submitted SNP assays in the MGI database.
Total RefSNPs (rs): Number of reference SNPs in the MGI database.
Assays per RefSNP (ss/rs) Average number of submitted SNP assays divided by the number of reference SNPs in the data load.
Total Strains with SNP data There are 86 strains, each of which should appear in the RefSNPs (rs) per Strain by Chromosome table. Strains without SNP data are not represented.
Assays (ss) per submitter Name of each submitter, linked to the submitter's details at dbSNP, followed by the number of assays submitted.
RefSNP s (rs) per Strain by Chromosome The table consists of:
  • a row for each of the 86 mouse strains, plus one at the top with the heading All Strains.
  • a column for each of the 21 mouse chromosomes.
Strains are sorted by total SNP count across all chromosomes. Strains appear in the same order as on the Mouse SNP Query Form.

Rows sum but columns do not.
  • The number in the All Chromosomes column (on the far right) is the sum of the row values beneath Chr 1 thru Chr Y (the first is the SNP total for All Strains, followed by the SNP totals per strain).
  • The number in the All Strains column (across the top) is NOT the sum of the SNP totals in the column beneath it: e.g., the SNPs on Chromosome 1 for all 86 strains do not add up to this number. This is because SNPs can be represented multiple times (i.e., when typed to multiple strains).


Why do the numbers returned by the query form differ from those in this summary?

When you use the Mouse SNP Query Form to search for SNPs search on a given strain or chromosome, the match is actually on the number of genome locations for SNPs returned.

Two examples:


How is this report sorted?

The default sort order for the MGI SNP Summary report is by strain. The 23 most common inbred strains appear in alphanumeric order, followed by a list of any additional mouse strains with strain allele data in dbSNP, in alphanumeric order.